Project description: Initial datasets shared by Australian collaborators (Tassiani Sarretto, Helena Anastacio). Three conditions (stem cells, cells grown for 7 and 14 days). 12 replicates per condition.
Date: 2023-05-30
Config: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/config_full_v2.yml
Notebook version: v0.2.0.post3+g966cb55.d20230408 (git-commit: 9f02807)
growthConditionsslideFalsereplicate_nb_overallNone/Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/anndatas/{slide}-well{well}-{row}{col}.h5adAnnDatas downloaded from Metaspace/Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/metadata_mod_full.csv| datasetName | datasetId | growthConditions | slide | row | col | replicate_nb_overall | group | submitter | PI | organism | organismPart | condition | mask_day_0 | mask_day_7 | mask_day_14 | well | ionisationSource | maldiMatrix | analyzer | resPower400 | polarity | uploadDateTime | FDR@10% | database | opticalImage | dataset_name | slide_batch_key | replicate_nb_per_slide_0 | replicate_nb_overall_0 | replicate_nb_per_slide_7 | replicate_nb_overall_7 | replicate_nb_per_slide | auto_generated_dataset_name | mask_slide_TS36 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | TS37 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h56m45s | 14 days | TS37 | C | 2 | 1 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:56:45.358 | 23 | HMDB - v4 | No optical image | TS37-well9-C2 | 1 | nan | nan | nan | nan | 1 | TS37-C2 | False |
| 1 | TS37 well8 top left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h55m41s | 14 days | TS37 | B | 2 | 2 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 8 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:55:41.764 | 127 | KEGG - v1 | No optical image | TS37-well8-B2 | 1 | nan | nan | nan | nan | 2 | TS37-B2 | False |
| 2 | TS37 well7 bottom left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h54m38s | 14 days | TS37 | A | 2 | 3 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:54:39.019 | 405 | HMDB - v4 | No optical image | TS37-well7-A2 | 1 | nan | nan | nan | nan | 3 | TS37-A2 | False |
| 3 | TS37 well3 middle right - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h54m03s | 14 days | TS37 | C | 1 | 4 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:54:03.789 | 120 | HMDB - v4 | No optical image | TS37-well3-C1 | 1 | nan | nan | nan | nan | 4 | TS37-C1 | False |
| 4 | TS37 well2 bottom right - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h53m25s | 14 days | TS37 | B | 1 | 5 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:53:25.910 | 227 | HMDB - v4 | No optical image | TS37-well2-B1 | 1 | nan | nan | nan | nan | 5 | TS37-B1 | False |
| 5 | TS37 well1 bottom left - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h52m46s | 14 days | TS37 | A | 1 | 6 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:52:46.833 | 3 | KEGG - v1 | No optical image | TS37-well1-A1 | 1 | nan | nan | nan | nan | 6 | TS37-A1 | False |
| 6 | TS38 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h24m02s | 14 days | TS38 | C | 2 | 7 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:24:02.680 | 355 | KEGG - v1 | No optical image | TS38-well9-C2 | 2 | nan | nan | nan | nan | 1 | TS38-C2 | False |
| 7 | TS38 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h17m43s | 14 days | TS38 | A | 1 | 8 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:17:43.298 | 312 | HMDB - v4 | No optical image | TS38-well1-A1 | 2 | nan | nan | nan | nan | 2 | TS38-A1 | False |
| 8 | TS38 well7- Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h22m51s | 14 days | TS38 | A | 2 | 9 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:22:51.341 | 180 | HMDB - v4 | No optical image | TS38-well7-A2 | 2 | nan | nan | nan | nan | 3 | TS38-A2 | False |
| 9 | TS38 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h19m54s | 14 days | TS38 | B | 1 | 10 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:19:54.395 | 296 | KEGG - v1 | No optical image | TS38-well2-B1 | 2 | nan | nan | nan | nan | 4 | TS38-B1 | False |
| 10 | TS38 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_06h21m37s | 14 days | TS38 | C | 1 | 11 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | True | False | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T06:21:37.336 | 117 | KEGG - v1 | No optical image | TS38-well3-C1 | 2 | nan | nan | nan | nan | 5 | TS38-C1 | False |
| 11 | TS35 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h15m20s | 7 days | TS35 | B | 2 | 1 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 8 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:15:20.200 | 64 | HMDB - v4 | No optical image | TS35-well8-B2 | 1 | nan | nan | 1.000000 | 1.000000 | 1 | TS35-B2 | False |
| 12 | TS35 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h17m05s | 7 days | TS35 | C | 2 | 2 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:17:06.036 | 46 | HMDB - v4 | No optical image | TS35-well9-C2 | 1 | nan | nan | 2.000000 | 2.000000 | 2 | TS35-C2 | False |
| 13 | TS35 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h10m32s | 7 days | TS35 | C | 1 | 3 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:10:32.445 | 274 | HMDB - v4 | No optical image | TS35-well3-C1 | 1 | nan | nan | 3.000000 | 3.000000 | 3 | TS35-C1 | False |
| 14 | TS35 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h11m11s | 7 days | TS35 | A | 2 | 4 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:11:11.516 | 43 | HMDB - v4 | No optical image | TS35-well7-A2 | 1 | nan | nan | 4.000000 | 4.000000 | 4 | TS35-A2 | False |
| 15 | TS35 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h09m40s | 7 days | TS35 | B | 1 | 5 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:09:40.107 | 138 | HMDB - v4 | No optical image | TS35-well2-B1 | 1 | nan | nan | 5.000000 | 5.000000 | 5 | TS35-B1 | False |
| 16 | TS35 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h08m38s | 7 days | TS35 | A | 1 | 6 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:08:38.102 | 66 | HMDB - v4 | No optical image | TS35-well1-A1 | 1 | nan | nan | 6.000000 | 6.000000 | 6 | TS35-A1 | False |
| 17 | TS36 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-02_01h43m22s | 7 days | TS36 | B | 2 | 7 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 8 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-02T01:43:22.810 | 52 | HMDB - v4 | No optical image | TS36-well8-B2 | 2 | nan | nan | 1.000000 | 7.000000 | 1 | TS36-B2 | True |
| 18 | TS36 well7- Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-02_01h42m25s | 7 days | TS36 | A | 2 | 8 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-02T01:42:25.784 | 264 | KEGG - v1 | No optical image | TS36-well7-A2 | 2 | nan | nan | 2.000000 | 8.000000 | 2 | TS36-A2 | True |
| 19 | TS36 well3 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-02_01h41m39s | 7 days | TS36 | C | 1 | 9 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-02T01:41:39.335 | 136 | KEGG - v1 | No optical image | TS36-well3-C1 | 2 | nan | nan | 3.000000 | 9.000000 | 3 | TS36-C1 | True |
| 20 | TS36 well1 -Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-02_01h40m13s | 7 days | TS36 | A | 1 | 10 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-02T01:40:13.578 | 252 | HMDB - v4 | No optical image | TS36-well1-A1 | 2 | nan | nan | 4.000000 | 10.000000 | 4 | TS36-A1 | True |
| 21 | TS36 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-02_01h40m56s | 7 days | TS36 | B | 1 | 11 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-02T01:40:56.194 | 133 | HMDB - v4 | No optical image | TS36-well2-B1 | 2 | nan | nan | 5.000000 | 11.000000 | 5 | TS36-B1 | True |
| 22 | TS36 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_05h43m12s | 7 days | TS36 | C | 2 | 12 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | True | False | True | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T05:43:12.895 | 127 | KEGG - v1 | No optical image | TS36-well9-C2 | 2 | nan | nan | 6.000000 | 12.000000 | 6 | TS36-C2 | True |
| 23 | TS33 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h14m46s | Stem cells | TS33 | B | 2 | 1 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | neuron | control | False | True | True | 8 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:14:46.823 | 228 | HMDB - v4 | No optical image | TS33-well8-B2 | 1 | 1.000000 | 1.000000 | nan | nan | 1 | TS33-B2 | False |
| 24 | TS33 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h15m58s | Stem cells | TS33 | C | 2 | 2 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:15:58.683 | 122 | HMDB - v4 | No optical image | TS33-well9-C2 | 1 | 2.000000 | 2.000000 | nan | nan | 2 | TS33-C2 | False |
| 25 | TS33 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h14m02s | Stem cells | TS33 | A | 2 | 3 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | neuron | control | False | True | True | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:14:02.055 | 147 | HMDB - v4 | No optical image | TS33-well7-A2 | 1 | 3.000000 | 3.000000 | nan | nan | 3 | TS33-A2 | False |
| 26 | TS33 well3 -Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h13m08s | Stem cells | TS33 | C | 1 | 4 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | neuron | control | False | True | True | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:13:08.967 | 32 | HMDB - v4 | No optical image | TS33-well3-C1 | 1 | 4.000000 | 4.000000 | nan | nan | 4 | TS33-C1 | False |
| 27 | TS33 well2 | 2023-02-01_02h11m55s | Stem cells | TS33 | B | 1 | 5 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | neuron | control | False | True | True | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:11:55.197 | 55 | HMDB - v4 | No optical image | TS33-well2-B1 | 1 | 5.000000 | 5.000000 | nan | nan | 5 | TS33-B1 | False |
| 28 | TS33 well1 | 2023-02-01_02h06m42s | Stem cells | TS33 | A | 1 | 6 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | neuron | control | False | True | True | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:06:42.827 | 193 | HMDB - v4 | No optical image | TS33-well1-A1 | 1 | 6.000000 | 6.000000 | nan | nan | 6 | TS33-A1 | False |
| 29 | TS34 well9 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h56m42s | Stem cells | TS34 | C | 2 | 7 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 9 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:56:42.389 | 49 | HMDB - v4 | No optical image | TS34-well9-C2 | 2 | 1.000000 | 7.000000 | nan | nan | 1 | TS34-C2 | False |
| 30 | TS34 well8 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h44m11s | Stem cells | TS34 | B | 2 | 8 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 8 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:44:11.325 | 40 | KEGG - v1 | No optical image | TS34-well8-B2 | 2 | 2.000000 | 8.000000 | nan | nan | 2 | TS34-B2 | False |
| 31 | TS34 well7 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h43m29s | Stem cells | TS34 | A | 2 | 9 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 7 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:43:29.710 | 46 | HMDB - v4 | No optical image | TS34-well7-A2 | 2 | 3.000000 | 9.000000 | nan | nan | 3 | TS34-A2 | False |
| 32 | TS34 well3_2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h41m43s | Stem cells | TS34 | C | 1 | 10 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 3 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:41:43.387 | 94 | HMDB - v4 | No optical image | TS34-well3-C1 | 2 | 4.000000 | 10.000000 | nan | nan | 4 | TS34-C1 | False |
| 33 | TS34 well2 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h39m48s | Stem cells | TS34 | B | 1 | 11 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 2 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:39:48.661 | 78 | HMDB - v4 | No optical image | TS34-well2-B1 | 2 | 5.000000 | 11.000000 | nan | nan | 5 | TS34-B1 | False |
| 34 | TS34 well1 - Fixed neuronal cells, 30um, positive ion mode, sublimation DHA | 2023-02-01_02h39m05s | Stem cells | TS34 | A | 1 | 12 | nan | Tassiani Sarretto | Shane Ellis | cultured cells | Skin | control | False | True | True | 1 | MALDI | DHA | Orbitrap | 120000 | positive | 2023-02-01T02:39:06.024 | 131 | HMDB - v4 | No optical image | TS34-well1-A1 | 2 | 6.000000 | 12.000000 | nan | nan | 6 | TS34-A1 | False |
| # pixels | # annotations | Comments/Suggestions | |
|---|---|---|---|
| After loading datasets in 'All Slides' jointly | 196311 | 80 | When few annotations are found at this stage, consider creating a custom Metaspace database |
| After selecting intra-cellular pixels | 58912 | 80 | If few pixels are left at this stage, you may need to adjust the `selection_metabolites` and `selection_threshold` parameters, and then download AnnDatas files again from Metaspace. See download summary report for more details about these parameters. |
| After filtering annotations found in less than 200 pixels and pixels with less than 20 annotations | 52722 | 80 | If not many pixels and/or annotations are left at this stage, you may need to adjust the parameters `min_pixels_per_annotation` and `min_annotations_per_pixel` |
Potential variance in UMAP associated with x/y position of well on slide
Potential variance in UMAP associated with slide number (independent on condition)
Circle size and number inside circles correspond to euclidean distance $D_{BIO}$ between the average PCA representation of biological label query and reference.
Circle size and number inside circles on the bottom row correspond to average pairwise distance $D_{REP}$ between replicates for individual biological labels, weighted by replicates' population sizes.
Circle fill color corresponds to the log2 ratio $R$ of $D_{BIO}$ to $D_{REP}$, according to $R=Log_{2}(D_{BIO}/D_{REP})$.
Note that while distances are symmetrical for query-reference pairs, $R$ is not due to division by $D_{REP}$.
A negative $R$ (i.e. a red circle) should raise your attention, as this will mean that the specific query group is closer to the query than the query's replicates are spaced from each other on average, indicating that technical variance is stronger than biological variance for these groups. Keep in mind to include your biological context into interpretation of this plot, as certain overlaps between conditions may be expected depending on biological labels.
Different clusters found by Leiden clustering are indicated by different colors in the following plot (in UMAP space):
The following plot indicates the Leiden cluster (colors) to which each pixels of a specific condition (one row of the plot) has been assigned:
The following plot indicates the condition (colors) to which each pixels of a specific Leiden cluster (one row of the plot) has been assigned:
The following plot shows the top 15 molecules that are most significantly differentially expressed between the different Leiden clusters:
7-days-cells¶The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster 7-days-cells:
14-days-cells¶The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster 14-days-cells:
Stem-cells¶The following UMAP plots show the intensities of the top 16 ions that are differentially expressed in Leiden cluster Stem-cells: